Unfortunately I have to confirm this (using 64-bit Linux Mint 18.2 MATE, which is based on Ubuntu 16.04 LTS) and looks like this prevents me of using Cryptomator at all as I am using Linux as my main system. In my case I tried to use VLC with Cryptomator and result was fatal - only reboot helped… Tried even newer kernel 4.12.11-041211-generic (64-bit) and this did not help either. This is unacceptable that in the middle of working just everything hangs and in my case I could not get no access until rebooted the computer. Cryptomator just said that one instance is running and it will exit:
[main] INFO org.cryptomator.launcher.Cryptomator - Starting Cryptomator 1.3.1 on Linux 4.12.11-041211-generic (amd64)
[main] WARN org.cryptomator.launcher.InterProcessCommunicator - System property cryptomator.ipcPortPath not set.
[main] DEBUG org.cryptomator.launcher.InterProcessCommunicator - Connecting to running process on TCP port 43667...
[main] INFO org.cryptomator.launcher.Cryptomator - Found running application instance. Shutting down.
But I could not have any access anymore through file manager or command-line. There were numerous different processes running by cryptomator and reboot was the fastest way to get system back.